Genomic and bioinformatic profiling of mutational neoepitopes reveals new rules to predict anticancer immunogenicity

Systematic identification of personal tumor-specific neoantigens in chronic lymphocytic leukemia

(2014) M. Rajasagi et al.   BLOOD

HLA-Binding Properties of Tumor Neoepitopes in Humans

(2014) E. F. Fritsch et al.   Cancer Immunology Research

Tumor Exome Analysis Reveals Neoantigen-Specific T-Cell Reactivity in an Ipilimumab-Responsive Melanoma

(2013) Nienke van Rooij et al.   JOURNAL OF CLINICAL ONCOLOGY

Mutated PPP1R3B Is Recognized by T Cells Used To Treat a Melanoma Patient Who Experienced a Durable Complete Tumor Regression

(2013) Y.-C. Lu et al.   JOURNAL OF IMMUNOLOGY

Accurate structure prediction of peptide–MHC complexes for identifying highly immunogenic antigens

(2013) Min-Sun Park et al.   MOLECULAR IMMUNOLOGY

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

snpTree - a web-server to identify and construct SNP trees from whole genome sequence data

(2012) Pimlapas Leekitcharoenphon et al.   BMC GENOMICS

Exploiting the Mutanome for Tumor Vaccination

(2012) J. C. Castle et al.   CANCER RESEARCH

RNA-seq analysis of prostate cancer in the Chinese population identifies recurrent gene fusions, cancer-associated long noncoding RNAs and aberrant alternative splicings

(2012) Shancheng Ren et al.   CELL RESEARCH

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

(2012) Andreas W. Götz et al.   Journal of Chemical Theory and Computation

Area under the curve as a tool to measure kinetics of tumor growth in experimental animals

(2012) Fei Duan et al.   JOURNAL OF IMMUNOLOGICAL METHODS

Cancer exome analysis reveals a T-cell-dependent mechanism of cancer immunoediting

(2012) Hirokazu Matsushita et al.   NATURE

Antigen Spreading Contributes to MAGE Vaccination-Induced Regression of Melanoma Metastases

(2011) Véronique Corbière et al.   CANCER RESEARCH

Loss of T Cell Antigen Recognition Arising from Changes in Peptide and Major Histocompatibility Complex Protein Flexibility

(2011) Francis K. Insaidoo et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Dynamical Characterization of Two Differentially Disease Associated MHC Class I Proteins in Complex with Viral and Self-Peptides

(2011) Daniele Narzi et al.   JOURNAL OF MOLECULAR BIOLOGY

Mouse genomic variation and its effect on phenotypes and gene regulation

(2011) Thomas M. Keane et al.   NATURE

Exome sequencing identifies GRIN2A as frequently mutated in melanoma

(2011) Xiaomu Wei et al.   NATURE GENETICS

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

(2011) Daniel Aird et al.   GENOME BIOLOGY

Anti–CTLA-4 Antibody Therapy: Immune Monitoring During Clinical Development of a Novel Immunotherapy

(2010) Margaret K. Callahan et al.   SEMINARS IN ONCOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Immune Rejection of Mouse Tumors Expressing Mutated Self

(2009) F. Duan et al.   CANCER RESEARCH

Modeling the Repertoire of True Tumor-Specific MHC I Epitopes in a Human Tumor

(2009) Nisheeth Srivastava et al.   PLoS One

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Accurate approximation method for prediction of class I MHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mers

(2008) C. Lundegaard et al.   BIOINFORMATICS

Epitope Landscape in Breast and Colorectal Cancer

(2008) N. H. Segal et al.   CANCER RESEARCH

Identification of Host Proteins Required for HIV Infection Through a Functional Genomic Screen

(2008) Abraham L. Brass et al.   SCIENCE

“It is the antigen(s), stupid” and other lessons from over a decade of vaccitherapy of human cancer

(2008) Matthew R. Buckwalter et al.   SEMINARS IN IMMUNOLOGY